Tag Archives: Data Analysis

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SINCERA – A Pipeline for Single-Cell RNA-Seq Profiling Analysis

SINCERA – A Pipeline for Single-Cell RNA-Seq Profiling Analysis

A major challenge in developmental biology is to understand the genetic and cellular processes/programs driving organ formation and differentiation of the diverse cell types that comprise the embryo. While recent studies using single cell transcriptome analysis illustrate the power to ...

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Bringing RNA-Seq into Undergraduate Education

Bringing RNA-Seq into Undergraduate Education

Virtual Workshop, June 2016 Cold Spring Harbor Laboratory’s DNA Learning Center (DNALC) invites you to apply to participate in a free 2-week online workshop for our NSF funded project, Infrastructure and Training to Bring Next-generation Sequence (NGS) Analysis Into Undergraduate ...

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Gene Codes releases Sequencher 5.4 – DNA Sequence Analysis Software

Gene Codes releases Sequencher 5.4 – DNA Sequence Analysis Software

ANN ARBOR, Mich.–(BUSINESS WIRE)– Gene Codes Corporation has announced the release of Sequencher 5.4, DNA Sequence Analysis Software. Sequencher 5.4 continues Gene Codes’ mission of empowering the bench scientist with the latest bioinformatics tools. Gene Codes has been developing Sequencher ...

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A new handbook for biologists – Using R at the Bench

A new handbook for biologists – Using R at the Bench

Using R at the Bench: Step-by-Step Data Analytics for Biologists, published by Cold Spring Harbor Laboratory Press and available in spiral bound hardcover and e-book formats, is a convenient bench-side handbook for biologists, designed as a handy reference guide for ...

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Digital Expression Explorer – RNA-seq analysis in minutes

Digital Expression Explorer – RNA-seq analysis in minutes

Researchers from the Baker IDI Heart and Diabetes Institute downloaded RNA-seq raw data from SRA, processed it and made it freely available on their webserver. http://dee.bakeridi.edu.au/ Learn how to analyse RNA-seq data sets in just a few minutes. No need ...

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List of RNA-Seq bioinformatics tools

List of RNA-Seq bioinformatics tools

from: https://en.wiki2.org/wiki/List_of_RNA-Seq_bioinformatics_tools 1 Quality control and pre-processing data 1.1 Quality control and filtering data 1.2 Detection of chimeric reads 1.3 Errors Correction 1.4 Pre-processing data 2 Alignment Tools 2.1 Short (Unspliced) aligners 2.2 Spliced aligners 2.2.1 Aligners based on known splice junctions (annotation-guided aligners) 2.2.2 De novo Splice Aligners 2.2.2.1 De novo Splice Aligners that also use annotation optionally 2.2.2.2 Other Spliced Aligners 3 Normalization, Quantitative analysis and Differential Expression 3.1 Multi-tool solutions 4 Workbench (analysis pipeline / integrated solutions) 4.1 Commercial Solutions 4.2 Open (free) Source Solutions 5 Alternative Splicing Analysis 5.1 General Tools 5.2 Intron Retention Analysis 6 Bias Correction 7 Fusion genes/chimeras/translocation finders/structural variations 8 Copy Number Variation identification 9 RNA-Seq simulators 10 Transcriptome assemblers 10.1 Genome-Guided assemblers 10.2 Genome-Independent (de novo) assemblers 10.2.1 Assembly evaluation tools 11 Co-expression networks 12 miRNA prediction 13 Visualization tools 14 Functional, Network & Pathway Analysis Tools 15 Further annotation tools for RNA-Seq data 16 RNA-Seq Databases 17 Webinars and Presentations ...

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